My only problem is that at the moment I can't get both books by folders and PRS Customizer optimalizations. I thought a sequence of

1) Copy new_opt to card
2) "Copy image from the card"
3) "Flash the image"
4) "Make a new image"
5) "Flash the image"
would do the trick, but it didn't. I'll try it again now to make sure I didn't make any mistake.

I went the other way around - extracting files from your image, comparing them to a PRS Customized image and modifying PRS Customizer files with your updates. In a minute or so I will know if I finally succeeded (the theory was fine all along, I just kept doing stupid mistakes such as copying your changes to a wrong file...).

Yep. Got it. I have a PRS-Customized Reader with Books By Folder! Will write a how-to in a few minutes.

Meanwhile, a few suggestions/bugreports:

1) I can't get Books by Folder to work on internal memory, even with your standard image. It just won't display any folders. SD card works fine, though.

2) It might be a good idea to place both autorun.js and addons/* to an extra directory. /Sony Reader or /database (since it has to exist anyway) would be a better starting point, IMHO. That way the internal memory will remain uncluttered by unneeded files and folders where they are in full view.

1) Books by Folder doesn't show the root of the IM, but the /database/media/books. If there are no other cards, the IM is chosen automatically.
2) The current structure is meant only for beta testing and quick updates. I am still not sure what's the best way for the release. Whether I'll keep the js files in IM or include them in /opt etc.